The potion crystals have been moved deep into ChromatiCraft's progression system. A few people have made spotlights on YouTube that you should be able to find (Reika hasn't put any of them on his website, for some reason) that explain the process fairly well.
In short:
1. Explore, explore, explore! You can find info fragments in two ways: In dungeon loot and whatnot, and by killing villagers, witches, or players with a pylon. Yes, you can learn things by committing suicide. There's probably some sort of cooldown on that, though, so people won't just set their bed by a pylon.
2. Shift-right-click your Chromic Lexicon (which you spawn with) to put fragments in. Right-click it without holding shift to open its GUI to read the info fragments.
3. Scroll around the Lexicon GUI with WASD or arrow keys. Hold shift to scroll faster.
4. The second tab on the left shows recipes (as does holding Control when clicking), and the top tab on the right contains hints as to progression, most of which involve looking at certain blocks or visiting certain locations. This will also reveal various plants around the landscape and ores underground that were previously invisible/looked like regular stone.
5. No clue what the other tab on the right does.
6. Potion crystals need the top tier casting complex, so you'll need to collect all four "Casting ____" info fragments as well as the one for potion crystals, level up your casting table to the highest tier (not sure if there's any way to tell what tier it's at) by crafting LOTS OF THINGS, and build lines of Repeaters to several (if not sixteen) different pylons.
7. If the potion crystals need boosted shards (can't remember if they do or not), make them by pouring a bucket of Liquid Chroma (XP + Chroma Collector) on the ground, throwing in about 24 tree berries of the same color (until they stop dissolving), throwing in a regular crystal shard, and waiting a few minutes. It shouldn't despawn, so you don't need to worry about that. Not sure if the berries need to be the same color as the shard.
